size <- 12. Later this will be the number of rows of the matrix.x <- rnorm( size ).x1 by adding (on average 10 times smaller) noise to x: x1 <- x + rnorm( size )/10.x and x1 should be close to 1.0: check this with function cor.x2 and x3 by adding (other) noise to x.size <- 12
x <- rnorm( size )
x1 <- x + rnorm( size )/10
cor( x, x1 )
[1] 0.9978864
x2 <- x + rnorm( size )/10
x3 <- x + rnorm( size )/10
x1, x2 and x3 column-wise into a matrix using m <- cbind( x1, x2, x3 ).m.m.heatmap( m, Colv = NA, Rowv = NA, scale = "none" ).m <- cbind( x1, x2, x3 )
class( m )
[1] "matrix"
head( m )
x1 x2 x3
[1,] 0.3385552 0.3009404 0.2999787
[2,] -0.3401840 -0.5357133 -0.5578792
[3,] 1.0900019 0.9287431 1.0052454
[4,] -1.4311247 -1.4135529 -1.2803936
[5,] 1.0218639 0.8277687 0.8339804
[6,] 0.2229762 0.2385809 0.3395296
heatmap( m, Colv = NA, Rowv = NA, scale = "none" ) # high is dark red, low is yellow
# x1, x2, x3 follow similar color pattern, they should be correlated
y1…y4 (but not correlated with x), of the same length size.m from columns x1…x3,y1…y4 in some random order.y <- rnorm( size )
y1 <- y + rnorm( size )/10
y2 <- y + rnorm( size )/10
y3 <- y + rnorm( size )/10
y4 <- y + rnorm( size )/10
m <- cbind( y4, y3, x2, y1, x1, x3, y2 )
heatmap( m, Colv = NA, Rowv = NA, scale = "none" ) # high is dark red, low is yellow
cc <- cor( m ) to build the matrix of correlation coefficients between columns of m.round( cc, 3 ) to show this matrix with 3 digits precision.cc <- cor( m )
round( cc, 3 ) #
y4 y3 x2 y1 x1 x3 y2
y4 1.000 0.987 -0.040 0.985 -0.021 -0.025 0.988
y3 0.987 1.000 -0.006 0.984 0.018 0.008 0.977
x2 -0.040 -0.006 1.000 0.045 0.996 0.998 -0.015
y1 0.985 0.984 0.045 1.000 0.066 0.060 0.988
x1 -0.021 0.018 0.996 0.066 1.000 0.995 0.006
x3 -0.025 0.008 0.998 0.060 0.995 1.000 0.007
y2 0.988 0.977 -0.015 0.988 0.006 0.007 1.000
heatmap( cc, symm = TRUE, scale = "none" )
# E.g. value for (row: x1, col: y1) is the corerlation of vectors x1, y1.
# Values of 1.0 are on the diagonal: e.g. x1 is perfectly correlated with x1.
# Correlations between x, x vectors are close to 1.0.
# Correlations between y, y vectors are close to 1.0.
# Correlations between x, y vectors are close to 0.0.
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